Check out GM Shankland's video series on the Najdorf, It's 8 or 9 lessons long and one entire 29 minute video is devoted to 6. Be3 e6.
How to GM's use Fritz to train

I can't imagine having any trouble playing against such a simple system like the najdorf. ...................ok, I can't carry the joke any further than that. Yeah, we've probably all had problems playing against it. If it makes you feel any better, it's not easy to be black using it, either. Heck, it's not easy to play either color with the najdorf.

I have had trouble playing against this system
of the najordoph (no clue how to spell it ) and I heard that GM's use fritz when preparing a line but then I realized that I couldn't figure out how they did it??
That's like saying you heard an artist used a brush to paint a world class picture, or an engineer used a calculator to put a satellite into orbit... but you can't figure it out yourself. Well of course.
Primarily, the GM uses their understanding of chess to find alternative moves and ideas. Then they use the engine to check different lines or positions. Sometimes they agree with the engine, sometimes they disagree.
So if you want to do this yourself, first develop a deep understanding of chess as a whole, and also the Najdorf specifically. Then you can use tools like engines to prepare lines like GMs do.
I have had trouble playing against this system
of the najordoph (no clue how to spell it
) and I heard that GM's use fritz when preparing a line but then I realized that I couldn't figure out how they did it??